Link to this post | posted 23 Feb, 2022 01:23
pia1@pitt.edu	I have not been able to get Phamerator to work since yesterday. When I try to google search phamerator, the search result seems to suggest that I'm not connected to WiFi (please see attached for the screenshot), but I actually do have a working WiFi. Can someone please help? 40Kb

Link to this post | posted 22 Feb, 2022 16:55
pia1@pitt.edu	I hate to be the pest but Phamerator is still not working for me. When I try to google search phamerator, the search result seems to suggest that I don't have WiFi (please see attached for the screenshot), but I actually do have a working WiFi. Chris, is there something that you have to do from your end to get it to work? 40Kb

Link to this post | posted 22 Feb, 2022 02:36
pia1@pitt.edu	I have tried WiFi at Pitt and at home, 3 different models of Mac and 1 PC, Firefox, Safari and Chrome, none of the above can get Phamerator to load for me. The following post https://seaphages.org/forums/topic/5097/ also discussed the 502 error, but it's not clear exactly how the issue was fixed…

Link to this post | posted 21 Feb, 2022 18:50
pia1@pitt.edu	I also tried both Firefox and Chrome. Neither worked for Phamerator. Same 502 error message.

Link to this post | posted 15 Feb, 2022 17:30

pia1@pitt.edu

Debbie and I just chatted about this particular phamm today. Debbie pointed out that this pham is particularly diverse and shared the multiple sequence alignment of all members in this pham, which is attached to this post. You may need a multiple sequence alignment viewer to open the alignment and Debbie recommended the following, https://macdownload.informer.com/aliview/ The AliView tool is free for download. To reiterate the important message again, Starterator does not have all the answers for choice of start site especially when a pham is very diverse. A closer look at the specific cluster to which the phage belongs may be more informative. In addition, the gene of interest, Pytheas gp29, appears to be a lysin B coding gene. Drs. Kim Payne (a former graduate student from the Hatful lab) and Graham Hatful have published a great article on the study of mycobacteriophage endolysins in PlosOne (https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0034052&type=printable). This article revealed the diversity and modular structure of endolysin and provides very helpful background knowledge on endolysin for annotation work. 38Kb

Link to this post | posted 15 Feb, 2022 16:28

pia1@pitt.edu

Hi Chris, Thanks so much for the in-depth discussion/explanation and advice! I really appreciate it! I wouldn't claim to have extensive experience with bioinformatics tools, but I am fully aware that no computational tool is 100% perfect. And chances are there are minor issues that are not necessarily worth fixing. In this case, I do NOT think the program "failed" at all. I'm just glad that I got clarifications from experts like you and thank you for putting this great tool to work in the first place!

Link to this post | posted 11 Feb, 2022 18:55
pia1@pitt.edu	Thank you both for replying! I agree with you, Debbie. Starterator by itself does not have all the answers. In this case, one of the two starts with the same number of MAs is actually not present in this gene. It really does not affect our analysis but I think we're just being extra nuanced. I'll email you to set up a time to chat.

Link to this post | posted 10 Feb, 2022 18:20
pia1@pitt.edu	Hi, This is regarding Pytheas gene 29 in the current version of Starterator report as of 02/10/22. My student caught the following and asked why start 44 is not the most annotated start since it has the same number of manual annotation as start 39. Please see attached slide for details. I don’t have the answer and would appreciate your input. Thank you! Ping An from University of Pittsburgh 349Kb

Link to this post | posted 18 Dec, 2021 14:48
pia1@pitt.edu	Thank you! Debbie. That is very helpful.

Link to this post | posted 17 Dec, 2021 14:19

pia1@pitt.edu

This is Ping An at University of Pittsburgh. I'm considering the function calls for genes 2, 3 and 4 of Meyran as terminase, 1 small subunit (gene 2) and 2 large subunits for ATPase domain (gene 3) and nuclease domain (gene 4), respectively. These tentative function calls are consistent with the current consensus for cluster DT phages. But I have some doubts, which seem to echo the two posts above. For gene 2, the best HHpred hit supporting terminase small subunit has a coverage of 45%. For gene 3, the top 5 strongest HHpred hits (probability over 90% and coverage at least 70%) are ATPase. Among these 5, 3 are also nuclease. For gene 4, top 10 strongest HHpred hits (probability over 90% and coverage at least 70%) are nuclease. Among these 10, 3 are also ATPase. Based on the above HHpred analysis, 1. Should gene 2 be assigned the function as “terminase small subunit”? 2. Should gene 3 and 4 be assigned specifically as terminase large subunit (ATPase) and (nuclease), respectively? I hope someone may provide some insights on the issue.